Trim stem end from squash. Cut about ⅓ off the top of each squash horizontally. Then cut a small horizontal sliver from the bottom so that the squash will sit flat and not roll. Dice the tops to ½ inch dice and set aside.
Using a small paring knife, cut around inside of squash then using a melon-baller, scoop out inside until the squash resembles a canoe. Try not to cut through to the bottom.
In a large skillet or frying pan heat the oil over medium heat. Add onion and cook two minutes. Add garlic, red pepper, mushrooms and cut up zucchini tops. Mix to combine and sauté one minute.
Remove from heat and mix in oregano, basil, parsley, salt, pepper, crumbs and both cheeses. Mix to combine.
Divide the filling between each zucchini boat and press into squash filling and pressing as you fill to hold shape.
Bake for 35 - 40 minutes uncovered. Try not to over cook, otherwise the zucchini will start to sag and the filling will not stay in.
As soon as they come out of the oven, sprinkle the tops with additional Parmesan cheese and serve.